\documentclass[12pt]{report}
\usepackage{uhthesis3}
\usepackage{booktabs}
\usepackage[small,bf]{caption}
\usepackage{graphicx}
\usepackage{subfig}
\usepackage{lscape}
\usepackage{algorithm}
\usepackage{algorithmic}
\usepackage{listings}
\usepackage[titletoc]{appendix}

\input{definitions.tex}
\setcounter{secnumdepth}{4}

\begin{document}

\title{\bf \large Mavis: Visualization Tool for Multiple Sequence Alignments}
\author{Lei Zhao}
\submitdate{August 2011} \degree{Master of Science}{Thesis}
\adviser{Dr. Yuriy Fofanov, Chairman\\
Department of Computer Science }
\firstreader{Dr. Dan Graur \\
Department of Biology and Biochemistry}
\secondreader{Dr. Shishir Shah\\
Department of Computer Science}
\threereadersfalse
\fourreadersfalse
\fivereadersfalse

\copyrightfalse \makecoverpages
\begin{acknowledgements}
\input{acknowledgements.tex}
\end{acknowledgements}

\begin{abstract}
\input{abstract.tex}
\end{abstract}
\setlength{\parskip}{.1 in}

\makecontentspages

\chapterpages
\newif \ifFIGS
\FIGSfalse

\input{chap1_Introduction.tex}
\input{chap2_Approach.tex}
\input{chap3_Algorithms.tex}
\input{chap4_Implementation.tex}
\input{chap5_Results.tex}
\input{chap6_Discussion.tex}
\input{chap7_Conclusion.tex}

\bibliographystyle{ieeetr}
\bibliography{references}

\appendix
\input{appendices.tex}

\end{document}
